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Here, we describe an algorithmic refinement of a spatial stochastic model of individuals and their communities.
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The results show that the algorithmic refinements improved the baseline in silico fragmentation performance, although it is difficult to tell which of the changes had the greatest influence.
Genome-scale metabolic networks provide a more accurate description of the metabolic processes of specific organisms, typically including manually curated physiological information as well as in silico algorithmic refinements.
We need an "algorithmic culture".
MetFrag has gone through algorithmic and scoring refinements.
The in silico fragmentation part of MetFrag2.2 has undergone extensive algorithmic and scoring refinements.
The heuristic we describe now is based on the C1P matrix recognition algorithm described in McConnell (2004), and relies on the very general algorithmic tool of partition refinement.
Our refinement algorithms are formulated within a maximum likelihood (ML) framework and focused solely on refinement--they are algorithmic boosters for one's preferred network inference method.
An important aspect of this pipeline is the feedback that constantly occurs between the computational and the experimental parts, which synergizes the refinement of both the algorithmic methodologies and the experimental protocols.
Furthermore, with continuous algorithmic improvement, the availability of faster hardware, and refinement of the available force fields addressing these limitations, the gap between simulations and experiments is rapidly closing, as evidenced by recent studies reporting simulations reaching time scales on the order of microseconds to submilliseconds.
Systematic refinements in binary imaging analysis techniques combined with an algorithmic approach allow for more exhaustive characterization of nerve parameters in the surgically relevant injury paradigms of regeneration following crush, transection, and nerve gap injuries.
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